Origin IGS: gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcggtatccctccgagtgccaccactaaatccaaagtatgagtgtaatccggtatcgaagaacaattcattactctgaacaagtggcaaaggtagtgcaaatcgaagacaatacgaaataaacccgtttatttctattgttgaggtgcagc Mask Tandem Repeat Region ================================================ gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Find is-nt database================================================ Query_seq: TF2229.1:TF2230|TF2229.1:TF2230:rteR regulatory ortholog (with internal stop):CTn excision protein:->->:2399788..2399938 151 gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2229.1:TF2230|TF2229.1:TF2230:rteR regulatory ortholog (with internal stop):CTn excision protein:->->:2399788..2399938 151 gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2229.1:TF2230|TF2229.1:TF2230:rteR regulatory ortholog (with internal stop):CTn excision protein:->->:2399788..2399938 151 gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 15 End: 149 .............. M E I N G F I S Y C L R F A L P L P L V Q S N E L F F D T G L H S Y F G F S G G T R R D T .. Protein_Len: 37 Strand: + Start: 40 End: 150 ....................................... M V F D L H Y L C H L F R V M N C S S I P D Y T H T L D L V V A L G G I P . Protein_Len: 30 Strand: - Start: 34 End: 123 ................................. K T N D E I Q V V K A V Q E S Y H I T R R Y R I V S M S Q M ............................ gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 82 Start: 53 End: 69 ....................................................GTGGCAAAGGTAGTGCA.................................................................................. gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2229.1:TF2230|TF2229.1:TF2230:rteR regulatory ortholog (with internal stop):CTn excision protein:->->:2399788..2399938 151 gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: tfor_TF2229.1_TF2230|rteR regulatory ortholog (with internal stop):CTn excision protein|POSITIVE:POSITIVE|[2399788,2399938]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga gctgcacctcaacaatagaaataaacgggtttatttcgtattgtcttcgatttgcactacctttgccacttgttcagagtaatgaattgttcttcgataccggattacactcatactttggatttagtggtggcactcggagggataccga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGCACCUCAACAAUAGAAAUAAACGGGUUUAUUUCGUAUUGUCUUCGAUUUGCACUACCUUUGCCACUUGUUCAGAGUAAUGAAUUGUUCUUCGAUACCGGAUUACACUCAUACUUUGGAUUUAGUGGUGGCACUCGGAGGGAUACCGA ..((((..((.((((((((((((((....)))))))).))))))....))..))))...(((((((((((.((((((((((.(((..(((..((((....))))..))).))))))))))))).....)))))))....))))........ (-44.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGUAUCCCUCCGAGUGCCACCACUAAAUCCAAAGUAUGAGUGUAAUCCGGUAUCGAAGAACAAUUCAUUACUCUGAACAAGUGGCAAAGGUAGUGCAAAUCGAAGACAAUACGAAAUAAACCCGUUUAUUUCUAUUGUUGAGGUGCAGC ((((.......)))).((((.(((((.....((.(((((((((((..(.((....)).)..)).))))).)))).))....)))))....)))).((((..((...(((((((.((((((((....)))))))))))))))))..)))).. (-37.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 146 102 151 108 tfor:TF2229|5end_CTn_excision_protein;_DNA_topoisomerase_IA_2397536..2397766_POSITIVE 333 150 102 113 74 tfor:TF2271|5end_conserved_hypothetical_protein_2435802..2436032_POSITIVE 306 50 1 171 119 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 302 150 101 130 78 tfor:TF2971|5end_possible_transposase_3178978..3179208_POSITIVE 293 67 24 100 53 tfor:TF2483|5end_hypothetical_protein_2659685..2659915_POSITIVE 290 141 102 49 6 tfor:TF2309|5end_cysteinyl-tRNA_synthetase_2468892..2469122_POSITIVE 290 140 91 145 81 tfor:TF1357|5end_hypothetical_protein_1437428..1437658_POSITIVE 283 150 116 184 153 tfor:TF2352|5end_phosphotransacetylase_2516688..2516918_POSITIVE 282 149 105 53 4 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 282 138 91 121 60 tfor:TF0023|5end_possible_response_element_in_two_component_regulation_19446..19676_POSITIVE 281 145 101 163 114 tfor:TF0357|5end_lysyl_endopeptidase_374517..374747_POSITIVE 279 150 111 113 79 tfor:TF2587|5end_hypothetical_protein_2751956..2752186_POSITIVE 278 150 101 68 8 tfor:TF0812|5end_conserved_hypothetical_protein_872087..872317_POSITIVE 275 97 54 51 3 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 275 105 62 152 100 tfor:TF0947|5end_extracellular_protease_990627..990857_POSITIVE 275 50 1 91 42 tfor:TF0008|5end_hypothetical_protein_4074..4304_POSITIVE 273 150 110 75 20 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 272 150 112 53 1 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 270 150 116 205 169 tfor:TF1433|5end_ribose_5-phosphate_isomerase_1517031..1517261_POSITIVE 267 84 48 202 173 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 146 102 88 45 tfor:TF2228|3end_CTn_excision_protein_2397553..2397703_POSITIVE 298 150 104 121 74 tfor:TF2617|3end_conserved_hypothetical_protein_2795172..2795322_POSITIVE 297 67 25 130 82 tfor:TF1144|3end_ABC_transporter,_ATP-binding/permease_component_1225301..1225451_POSITIVE 290 140 91 91 27 tfor:TF1356|3end_cysteine_synthase_A_1437454..1437604_POSITIVE 282 138 91 117 56 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 280 149 101 151 101 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 279 150 111 141 107 tfor:TF2586|3end_conserved_hypothetical_protein_2752064..2752214_POSITIVE 278 150 101 82 22 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 275 97 54 51 3 tfor:TF2788|3end_hypothetical_protein_2972511..2972661_POSITIVE 275 149 103 79 34 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 275 105 62 143 91 tfor:TF0946|3end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_990698..990848_POSITIVE 275 50 1 110 61 tfor:TF0009|3end_transcriptional_regulator_4173..4323_POSITIVE 272 150 112 135 83 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 271 150 123 48 14 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 270 150 116 84 48 tfor:TF1432|3end_possible_hemolysin_A_1516990..1517140_POSITIVE 269 69 24 74 23 tfor:TF1242|3end_3-methyl-2-oxobutanoate_hydroxymethyltransferase_1327114..1327264_POSITIVE 269 147 102 141 99 tfor:TF0107|3end_ion_channel_protein_115093..115243_POSITIVE 265 137 92 72 24 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE 265 78 34 64 16 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 262 134 91 139 93 tfor:TF1840|3end_transposase_1991416..1991566_POSITIVE